Biofundamentals 2e

by Klymkowsky & Cooper

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Biofundamentals is an attempt to build a more conceptually coherent, rigorous and engaging introductory course in modern biology. An introduction to core the observations, concepts and scientific principles in biology, centered on molecular mechanisms & cellular processes and their application in evolution, development & human health

Description from LibreTexts.

Publisher
University of Colorado Boulder & Michigan State University
Subjects
Biology, Cell and Molecular Biology
Licence
CC BY-NC-SA 4.0, as LibreTexts states it. Non-commercial use only.
Who can read
Tweens profiles and older, judged from its title and subjects

Contents

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  1. Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. 1: Understanding Science and Thinking Scientifically
  7. 1.0: Introduction
  8. 1.1: The interconnectedness (self-consistency) of science
  9. 1.2: Models, Hypotheses, and Theories
  10. 1.3: Science is Social
  11. 1.4: Teaching and Learning Science
  12. 1.5: Understanding Scientific Ideas
  13. 2: Life’s Diversity and Origins
  14. 2.0: Introduction
  15. 2.1: What is life, exactly?
  16. 2.2: The cell theory and the continuity of life
  17. 2.3: The organization of organisms
  18. 2.4: Spontaneous generation and the origin of life
  19. 2.5: The Death of Vitalism
  20. 2.6: Thinking about life’s origins
  21. 2.7: Experimental studies on the origins of life
  22. 2.8: Mapping the history of life on earth
  23. 2.9: Fossil evidence for the history of life on earth
  24. 2.10: Life's impact on earth
  25. 3: Evolutionary Mechanisms and the Diversity of Life
  26. 3.0: Introduction
  27. 3.1: Organizing organisms (hierarchically)
  28. 3.2: Natural and un-natural groups
  29. 3.3: Fossils and family relationships- introducing cladistics
  30. 3.4: Evolution theory’s core concepts
  31. 3.5: Limits on populations
  32. 3.6: Darwin and Wallace's conceptual leap
  33. 3.7: Mutations and the origins of genotype-based variation
  34. 3.8: The origins of polymorphisms
  35. 3.9: Genotype-phenotype relationships- discrete and continuous traits
  36. 3.10: Variation, selection, and speciation
  37. 3.11: Types of simple selection
  38. 3.12: Considering stochastic processes
  39. 3.13: Genetic diversity, population size, founder effects and population bottlenecks
  40. 3.14: Population bottlenecks
  41. 3.15: Genetic drift
  42. 3.16: Gene linkage- one more complication
  43. 3.17: A brief reflection on the complexity of phenotypic traits
  44. 3.18: Speciation and extinction
  45. 3.19: Mechanisms of speciation
  46. 3.20: Mechanisms of reproductive isolation
  47. 3.21: Sympatric speciation
  48. 3.22: Signs of evolution- homology and convergence
  49. 3.23: Homologies provide evidence for a common ancestor
  50. 3.24: Anti-evolution arguments
  51. 4: Social Evolution and Sexual Selection
  52. 4.0: Introduction
  53. 4.1: Selecting social (cooperative) traits
  54. 4.2: Quorum Sensing
  55. 4.3: Active (altruistic) cell death
  56. 4.4: Inclusive fitness, kin and group selection, and social evolution
  57. 4.5: Group selection
  58. 4.6: Defense against social cheaters
  59. 4.7: The appearance of multicellular organisms
  60. 4.8: Origins and implications of sexual reproduction
  61. 4.9: Sexual dimorphism
  62. 4.10: Sexual Selection
  63. 4.11: Curbing runaway selection
  64. 5: Molecular Interactions, Thermodynamics and Reaction Coupling
  65. 5.0: Introduction
  66. 5.1: Approaching Thermodynamics
  67. 5.2: Coupling thermodynamically favorable and unfavorable reactions
  68. 5.3: Reaction rates
  69. 5.4: Coupling Reactions
  70. 5.5: Inter- and intra-molecular interactions
  71. 5.6: Covalent bonds
  72. 5.7: Bond Stability and Thermal Motion (a non-biological moment)
  73. 5.8: Bond polarity, inter- and intramolecular interactions
  74. 5.9: The implications of bond polarity
  75. 5.10: Interacting with Water
  76. 6: Membrane Boundaries and Capturing Energy
  77. 6.0: Introduction
  78. 6.1: Defining the Cell’s Boundary
  79. 6.2: The origin of biological membranes
  80. 6.3: Transport across membranes
  81. 6.4: Channels and carriers
  82. 6.5: Generating gradients- using coupled reactions and pumps
  83. 6.6: Simple Phototrophs
  84. 6.7: Chemo-osmosis (an overview)
  85. 6.8: Oxygenic Photosynthesis
  86. 6.9: Chemotrophs
  87. 6.10: Using the energy stored in membrane gradients
  88. 6.11: Osmosis and living with and without a cell wall
  89. 6.12: An evolutionary scenario for the origin of eukaryotic cells
  90. 6.13: Making a complete eukaryote
  91. 7: The Molecular Nature of Heredity
  92. 7.0: Introduction
  93. 7.1: Discovering how nucleic acids store genetic information
  94. 7.2: Locating hereditary material within the cell
  95. 7.3: Identifying DNA as the genetic material
  96. 7.4: Unraveling Nucleic Acid Structure
  97. 7.5: Discovering the structure of DNA
  98. 7.6: DNA, sequences, and information
  99. 7.7: Discovering RNA- structure and some functions
  100. 7.8: DNA Replication
  101. 7.9: Replication machines
  102. 7.10: Further replication complexities
  103. 7.11: Mutations, Deletions, Duplications and Repair
  104. 7.12: Genes and alleles
  105. 7.13: The origin of new (de novo) genes
  106. 7.14: DNA repeat diseases and genetic anticipation
  107. 8: Peptide Bonds, Polypeptides and Proteins
  108. 8.0: Introduction
  109. 8.1: Specifying a polypeptide’s sequence
  110. 8.2: The origin of the genetic code
  111. 8.3: Protein synthesis- transcription (DNA to RNA)
  112. 8.4: Protein synthesis- translation (RNA to polypeptide)
  113. 8.5: The translation (polypeptide synthesis) cycle
  114. 8.6: Effects of point mutations on polypeptides and proteins
  115. 8.7: Getting more complex- gene regulation in eukaryotes
  116. 8.8: Turning polypeptides into proteins
  117. 8.9: Regulating protein activity, concentrations, and stability (half-life)
  118. 8.10: Allosteric and post-translational regulation
  119. 8.11: Diseases of folding and misfolding
  120. 8.12: Molecular machines
  121. 9: Genomes, Genes and Regulatory networks
  122. 9.0: Introduction
  123. 9.1: Locating information within DNA
  124. 9.2: Enhancers and transcription start and stop sites
  125. 9.3: Interaction networks and model systems
  126. 9.4: E. coli as a model system
  127. 9.5: Adaptive behavior and gene networks- the lac response
  128. 9.6: Types of regulatory interactions
  129. 9.7: Final thoughts on (molecular) noise
  130. 10: Social Systems
  131. 10.0: Introduction
  132. 10.1: Targeting membrane proteins to where they need to be
  133. 10.2: Nuclear targeting and exclusion
  134. 10.3: Intercellular signaling- signals, receptors and responses
  135. 10.4: Signaling molecules and receptors
  136. 10.5: Cellular reprogramming- embryonic and induced pluripotent stem cells
  137. 11: Cellular reproduction and horizontal gene transfer in prokaryotes
  138. 11.0: Introduction
  139. 11.1: What counts as sex in prokaryotes
  140. 11.2: Other naturally occurring horizontal gene transfer mechanisms
  141. 12: Asexual and Sexual Reproduction in Eukaryotes
  142. 12.0: Introduction
  143. 12.1: Ploidy during the cell cycle
  144. 12.2: Monitoring cellular processes- mitosis
  145. 12.3: Sex-determination and its chromosomal basis
  146. 12.4: Steps in meiosis- from diploid to haploid
  147. 12.5: Recombination and independent segregation
  148. 12.6: Linkage and haplotypes
  149. 12.7: X-inactivation and sex-linked traits
  150. 12.8: X-linked diseases and mono-allelic gene expression
  151. 13: How Alleles Arise - Mutations
  152. 13.0: Introduction
  153. 13.1: Mutations into alleles
  154. 13.2: Luria and Delbrück- Discovering the origin of mutations
  155. 13.3: Forward and reverse genetics
  156. 13.4: Generating specific mutations on demand - CRISPR-Cas9 and related technologies
  157. 13.5: Longer term mutation and evolution studies
  158. 14: Somatic Mutations and Genome Dynamics
  159. 14.0: Introduction
  160. 14.1: Rates and effects of somatic mutation
  161. 14.2: Non-disjunction- aberrant chromosome segregation
  162. 14.3: Genome dynamics
  163. 14.4: Gene duplications and deletions
  164. 14.5: Orthologs and paralogs
  165. 14.6: Transposons- moving DNA within a genome (and weird genetics)
  166. 15: Mendel and Weldon - Contexts and their Effects on Phenotypes
  167. 15.0: Introduction
  168. 15.1: How Mendel did what he did
  169. 15.2: Weldon's critique
  170. 15.3: Chi square (?2) analysis, hypothesis testing, and small numbers
  171. 15.4: Dihybrid crosses- linkage and recombination
  172. 15.5: Genetic complementation
  173. 15.6: Interacting traits- synthetic lethality and co-dominance
  174. 15.7: Interacting traits- epistasis
  175. 15.8: Maternal and paternal effects
  176. 15.9: Mitochondrial inheritance
  177. 15.10: Imprinting- conflicts between mother, father, and fetus
  178. 15.11: Estimating the number of genes involved in a particular traits
  179. 15.12: On the nature of mutations (again)
  180. 15.13: Alleles, traits, and genetic diseases in humans.
  181. 15.14: Concordance between monozygotic twins and genetic influence on a trait
  182. 15.15: Measuring evolution’s impact on allele frequencies- Hardy-Weinberg
  183. 15.16: Genetic anticipation
  184. 15.17: The persistence of deleterious alleles
  185. 16: Tools for Studying Genes and Genomes
  186. 16.0: Introduction
  187. 16.1: Synteny examined using Genomicus
  188. 16.2: Where is a gene expressed?
  189. 16.3: Using web-based bioinformatic tools- gnomAD
  190. 16.4: Using web-based bioinformatic tools- BLAST
  191. 16.5: Genome-wide Association Studies (GWAS)
  192. 17: Supplemental Chapter - Fundamental concepts and developing systems
  193. 17.0: Introduction
  194. 17.1: How do systems change at the molecular level?
  195. 17.2: Steady state and changing molecular concentrations- synthesis and degradation
  196. 17.3: Direct and indirect cellular responses to signaling molecules
  197. 17.4: Modeling gene expression
  198. 17.5: Reversible, irreversible, and cascade effects
  199. 18: Supplemental Chapter - Social interactions between cells
  200. 18.0: Introduction
  201. 18.1: How do unicellular organisms generate phenotypic diversity?
  202. 18.2: Dying for others – social interactions between “unicellular” organisms
  203. 18.3: Quorum effects (somewhat redundant)
  204. 18.4: Transient and clonal ("true") metazoans
  205. 18.5: Unicellular to multicellularity to unicellularity
  206. 18.6: Evolutionary origins of clonal (permanent) multicellularity
  207. 19: Supplemental Chapter - The role of model systems in understanding metazoan development
  208. 19.0: Introduction
  209. 19.1: Model Systems
  210. 19.2: Some model systems
  211. 19.3: Frogs and fish
  212. 19.4: Chick and Quail
  213. 19.5: The fruit fly Drosophila melanogaster
  214. 19.6: The nematode Caenorhabditus elegans
  215. 19.7: The Mouse
  216. 19.8: ESC and iPSC derived organoids
  217. 20: Appendix- Muller’s Morphs
  218. Back Matter
  219. Index
  220. Glossary
  221. Detailed Licensing